Using Delaunay triangulation to sample whole‐specimen color from digital images

1. Color variation is one of the most obvious examples of variation in nature, but biologically meaningful quantification and interpretation of variation in color and complex patterns are challenging. Many current methods for assessing variation in color patterns classify color patterns using categorical measures and provide aggregate measures that ignore spatial pattern, or both, losing potentially important aspects of color pattern.
2. Here, we present Colormesh, a novel method for analyzing complex color patterns that offers unique capabilities. Our approach is based on unsupervised color quantification combined with geometric morphometrics to identify regions of putative spatial homology across samples, from histology sections to whole organisms. Colormesh quantifies color at individual sampling points across the whole sample.
3. We demonstrate the utility of Colormesh using digital images of Trinidadian guppies (Poecilia reticulata), for which the evolution of color has been frequently studied. Guppies have repeatedly evolved in response to ecological differences between up‐ and downstream locations in Trinidadian rivers, resulting in extensive parallel evolution of many phenotypes. Previous studies have, for example, compared the area and quantity of discrete color (e.g., area of orange, number of black spots) between these up‐ and downstream locations neglecting spatial placement of these areas. Using the Colormesh pipeline, we show that patterns of whole‐animal color variation do not match expectations suggested by previous work.
4. Colormesh can be deployed to address a much wider range of questions about color pattern variation than previous approaches. Colormesh is thus especially suited for analyses that seek to identify the biologically important aspects of color pattern when there are multiple competing hypotheses or even no a priori hypotheses at all.

     

Identification of candidate AFLP markers for shell color of the Pacific oyster (Crassostrea gigas) under artificial selection

The shell color of the Pacific oyster (Crassostrea gigas) is a desirable trait, but only a few genetic studies on shell color have been documented. Through successive selective breeding, four shell color variants of white (W), gold (G), black (B) and purple (P) C. gigas have been developed. The amplified fragment length polymorphism (AFLP) technique was used to scan the genomes of the four variants with different shell colors and one wild population (C) to identify candidate markers for shell polymorphism. Fifteen AFLP primer combinations were used, 1079 loci were scored as polymorphic loci, and the percentage of polymorphic bands was 95.5%. In the gold, white, black, purple and wild populations, the percentages of polymorphic loci were estimated to be 90.5% (G), 90.0% (W), 91.1% (B), 95.3% (P) and 93.2% (C); the expected heterozygosity values were 0.3115 (G), 0.3044 (W), 0.3102 (B), 0.3285 (P) and 0.3105 (C). The white shell variant was observed to have slightly lower genetic diversity than others, with a F_ST value of 0.1483. These results indicated that the four different shell color variants had high genetic diversity and that the genetic differentiation of populations mostly results from genetic diversity of individuals within populations. Furthermore, 11 outlier loci were considered candidate markers for shell color. This work provides new insights on relationships among color variants of C. gigas.     

A preliminary study for identification of candidate AFLP markers under artificial selection for shell color in pearl oyster Pinctada fucata

Pearl oyster Pinctada fucata is widely cultured to produce seawater pearl in South China, and the quality of pearl is significantly affected by its shell color. Thus the Pearl Oyster Selective Breeding Program (POSBP) was carried out for the shell color and growth traits. The black (B), gold (G), red (R) and white (W) shell strains with fast growth trait were achieved after five successive generation selection. In this study, AFLP technique was used to scan genome of four strains with different shell colors to identify the candidate markers under artificial selection. Eight AFLP primer combinations were screened and yielded 688 loci, 676 (98.26%) of which were polymorphic. In black, gold, red and white strains, the percentage of polymorphic loci was 90.41%, 87.79%, 93.60% and 93.31%, respectively, Nei's gene diversity was 0.3225, 0.2829, 0.3221 and 0.3292, Shannon's information index was 0.4801, 0.4271, 0.4825 and 0.4923, and the value of F_ST was 0.1805. These results suggested that the four different shell color strains had high genetic diversity and great genetic differentiation among strains, which had been subjected to the continuous selective pressures during the artificial selective breeding. Furthermore, six outlier loci were considered as the candidate markers under artificial selection for shell color. This study provides a molecular evidence for the inheritance of shell color of P. fucata.     

Identification and Mapping of Amplified Fragment Length Polymorphism Markers Linked to Shell Color in Bay Scallop, Argopecten irradians irradians (Lamarck, 1819)

Amplified fragment length polymorphisms (AFLP) were used to study the inheritance of shell color in Argopecten irradians. Two scallops, one with orange and the other with white shells, were used as parents to produce four F₁ families by selfing and outcrossing. Eighty-eight progeny, 37 orange and 51 white, were randomly selected from one of the families for segregation and mapping analysis with AFLP and microsatellite markers. Twenty-five AFLP primer pairs were screened, yielding 1138 fragments, among which 148 (13.0%) were polymorphic in two parents and segregated in progeny. Six AFLP markers showed significant (P < 0.05) association with shell color. All six loci were mapped to one linkage group. One of the markers, F1f335, is completely linked to the gene for orange shell, which we designated as Orange1, without any recombination in the progeny we sampled. The marker was amplified in the orange parent and all orange progeny, but absent in the white parent and all the white progeny. The close linkage between F1f335 and Orange1 was validated using bulk segregation analysis in two natural populations, and all our data indicate that F1f335 is specific for the shell color gene, Orange1. The genomic mapping of a shell color gene in bay scallop improves our understanding of shell color inheritance and may contribute to the breeding of molluscs with desired shell colors.     

A simple method for two-dimensional color analyses of plant leaves

Coloration and color pattern are basic information for plant physiology, ecology, and taxonomy. Until recently, such color analysis of biological materials required expensive equipment. Here we report a convenient method for analyzing color of plant leaves with ImageJ, free software. Color digital images of croton leaves were divided with ImageJ into Red, Green, and Blue images, and then exported as two-dimensional numeric data. After processing images with Adobe Photoshop Elements and Microsoft Excel, color patterns were obtained as histograms. A comparison of the histograms evaluated characteristics of croton leaf variegation. The method successfully quantified color information of the plant leaves with an inexpensive PC set. Apart from taxonomic applications, the simple algorithms allow application of the present methodology to various types of color and color pattern analyses. Published in Russian in Fiziologiya Rastenii, 2006, Vol. 53, No. 1, pp. 139–147. The text was submitted by the authors in English.     

Spatial patterns of correlated scale size and scale color in relation to color pattern elements in butterfly wings

Complex butterfly wing color patterns are coordinated throughout a wing by unknown mechanisms that provide undifferentiated immature scale cells with positional information for scale color. Because there is a reasonable level of correspondence between the color pattern element and scale size at least in Junonia orithya and Junonia oenone, a single morphogenic signal may contain positional information for both color and size. However, this color–size relationship has not been demonstrated in other species of the family Nymphalidae. Here, we investigated the distribution patterns of scale size in relation to color pattern elements on the hindwings of the peacock pansy butterfly Junonia almana, together with other nymphalid butterflies, Vanessa indica and Danaus chrysippus. In these species, we observed a general decrease in scale size from the basal to the distal areas, although the size gradient was small in D. chrysippus. Scales of dark color in color pattern elements, including eyespot black rings, parafocal elements, and submarginal bands, were larger than those of their surroundings. Within an eyespot, the largest scales were found at the focal white area, although there were exceptional cases. Similarly, ectopic eyespots that were induced by physical damage on the J. almana background area had larger scales than in the surrounding area. These results are consistent with the previous finding that scale color and size coordinate to form color pattern elements. We propose a ploidy hypothesis to explain the color–size relationship in which the putative morphogenic signal induces the polyploidization (genome amplification) of immature scale cells and that the degrees of ploidy (gene dosage) determine scale color and scale size simultaneously in butterfly wings.     

Biological color stripping: A novel technology for removal of dye from cellulose fibers

This research work was carried out to compare the color stripping efficiency of optimized biological method with the chemical stripping, commonly employed in the textile industries. Knitted fabric dyed with Reactive black B dye in 2, 4 and 6% shades strengths was subjected to chemical and biological stripping processes individually. Biological stripping process was found many fold superior to chemical one. It was noted that shade strength does not showed any pronounced effect on the bursting strength of fabric but biological and chemical treatment affect the quality of fabrics in terms of bursting strength/durability of fabric. White rot fungus Ganoderma lucidum IBL-05 showed good potential for decolorization/color stripping of cotton fabric dyed with Reactive black B under optimized set of conditions. The chemical stripping technology is inferior to biological stripping process regarding the quality of fabric and percent color removal from cotton fabric dyed with Reactive black B dye.     

Technical note: quantitative measures of iris color using high resolution photographs

Our understanding of the genetic architecture of iris color is still limited. This is partly related to difficulties associated with obtaining quantitative measurements of eye color. Here we introduce a new automated method for measuring iris color using high resolution photographs. This method extracts color measurements in the CIE 1976 L*a*b* (CIELAB) color space from a 256 by 256 pixel square sampled from the 9:00 meridian of the iris. Color is defined across three dimensions: L* (the lightness coordinate), a* (the red-green coordinate), and b* (the blue-yellow coordinate). We applied this method to a sample of individuals of diverse ancestry (East Asian, European and South Asian) that was genotyped for the HERC2 rs12913832 polymorphism, which is strongly associated with blue eye color. We identified substantial variation in the CIELAB color space, not only in the European sample, but also in the East Asian and South Asian samples. As expected, rs12913832 was significantly associated with quantitative iris color measurements in subjects of European ancestry. However, this SNP was also strongly associated with iris color in the South Asian sample, although there were no participants with blue irides in this sample. The usefulness of this method is not restricted only to the study of iris pigmentation. High-resolution pictures of the iris will also make it possible to study the genetic variation involved in iris textural patterns, which show substantial heritability in human populations.     

The role of MC1R gene in buffalo coat color

Melanocortin-1 receptor (MC1R) plays a major role in pigmentation in many species. To investigate if the MC1R gene is associated with coat color in water buffalo, the coding region of MC1R gene of 216 buffalo samples was sequenced, which included 49 black river buffalo (Murrah and Nili-Ravi), 136 swamp buffalo (Dehong, Diandongnan, Dechang, Guizhou, and Xilin) with white and gray body, and 31 hybrid offspring of river buffalo Nili-Ravi (or Murrah) and swamp buffalo. Among the three variation sites found, SNP684 was synonymous, while SNP310 and SNP384 were nonsynonymous, leading to p.S104G and p.I128M changes, respectively. Only Individuals carrying homozygote EBR/EBR were black. The genotype and phenotype analysis of the hybrid offspring of black river buffalo and gray swamp buffalo further revealed that the river buffalo type allele EBR or the allele carrying the amino acid p.104S was important for the full function of MC1R. The in silico functional analysis showed that the amino acid substitutions p.G104S and p.M128I had significant impact on the function of MC1R. Above results indicate that the allele EBR or the allele carrying the amino acid p.104S was associated with the black coat color in buffalo.     

Morphological studies on the Sulawesi macaques I: Phyletic analysis of body color

The body color of Sulawesi macaques was measured quantitatively and compared among the different monkeys. As a result, divergence models for extant Sulawesi macaques, withtonkeana as the starting point and fading as the sole direction of color change, were inferred as follows: (1) fading slightly on the upper half of the body—nigra, fading more on the proximal part of the body—nigrescens; (2) fading over the whole body—maura; (3) fading greatly on the legs—hecki; and (4) fading on the distal part of the body—ochreata, fading more over the whole body, including the proximal part of the body—brunnescens. The color changed progressively in the order of (1) through (4). The divergence model, excluding the position ofhecki (3), supports the speciation model ofFooden (1969). If the proto-Sulawesi macaques had a body color pattern similar to the livingnemestrina, darkening would have been necessary for the evolution of the Sulawesi macaques after their immigration, and it may have been acquired as an adaptation to the ground (forest floor) living nature of the Sulawesi macaques, together with influences deriving from the insularity and/or from the absence of predators.     

Population heterogeneity and color stimulus heterogeneity in agent-based color categorization

Investigating the interactions between universal and culturally specific influences on color categorization across individuals and cultures has proven to be a challenge for human color categorization and naming research. The present article simulates the evolution of color lexicons to evaluate the role of two realistic constraints found in the human phenomenon: (i) heterogeneous observer populations and (ii) heterogeneous color stimuli. Such constraints, idealized and implemented as agent categorization and communication games, produce interesting and unexpected consequences for stable categorization solutions evolved and shared by agent populations. We find that the presence of a small fraction of color deficient agents in a population, or the presence of a “region of increased salience” in the color stimulus space, break rotational symmetry in population categorization solutions, and confine color category boundaries to a subset of available locations. Further, these heterogeneities, each in a different, predictable, way, might lead to a change of category number and size. In addition, the concurrent presence of both types of heterogeneity gives rise to novel constrained solutions which optimize the success rate of categorization and communication games. Implications of these agent-based results for psychological theories of color categorization and the evolution of color naming systems in human societies are discussed.     

山樱花品种间花色差异的代谢组学研究

山樱花是世界著名的观花类植物，花色是其最重要的观赏特征。为探究影响山樱花品种间花色差异的代谢通路及关键代谢产物变化，该文利用LC-MS/MS技术对白色、绿色和粉色的山樱花品种进行花青素靶向代谢组学比较分析。结果表明：(1)共检测到42种花青素物质，主要包含矮牵牛素、飞燕草素、黄酮类化合物、锦葵色素、芍药花素、矢车菊素、天竺葵素和原花青素8种物质。(2)差异代谢花青素25种，包括11种下调、14种上调，其中有7种花青素在粉色花瓣中显著富集。(3)KEGG通路注释发现差异代谢物在花青素生物合成通路中显著富集，结合聚类结果发现矮牵牛素-3-O-葡萄糖苷是山樱花品种间花色差异产生的关键代谢物。该研究揭示了山樱花花色差异的代谢机理，为后续山樱花花色分子调控机制研究提供了一定的理论依据，也为新品种花色改良和选育提供了一定的科学参考。     

Bird-pollinated Macaronesian Lotus (Leguminosae) evolved within a group of entomophilous ancestors with post-anthesis flower color change

We analyzed the evolution of red/orange flowers in four putatively bird-pollinated species of Macaronesian Lotus, with the aim of investigating whether this floral trait evolved from a similar trait found in some entomophilous Lotus species, namely the ability to modify flower color to red after anthesis. First, we mapped the ability to modify flower color in this group on a well-resolved and densely sampled phylogenetic tree of the Macaronesian Lotus. Secondly, we determined differences in light reflectance and pigment composition between petals of (1) prechange and postchange flowers in bee-pollinated species and (2) between bee and putatively bird-pollinated species. Post-anthesis flower color change evolved three times within Macaronesian Lotus, and putatively bird-pollinated species evolved within a clade with this ability to change flower color to red after anthesis. The evolutionary transition to red/orange flowers in the putatively bird-pollinated species involved biochemical changes similar to those of the developmental transition to red postchange flowers. In both cases there are changes in the composition of flavonols and anthocyanidins within the same metabolic pathways, especially in the cyanidin branch of pigment production, but not the activation or inactivation of additional branches of this pathway. Post-anthesis color change in Lotus, from yellow to red, is thought to be an adaptation to reduce bee visits to already pollinated flowers. Our results are consistent with the hypothesis that constitutive red coloration for bird-pollination evolved from facultative red flower color change in Lotus. As red post-anthesis coloration is widespread in plants, this may possibly represent a widespread exaptive mechanism for the evolution of bird pollination.     

Shell morphology and color of the subtidal whelk Buccinum undatum exhibit fine‐scaled spatial patterns

Geographical patterns in morphology can be the result of divergence among populations due to neutral or selective changes and/or phenotypic plasticity in response to different environments. Marine gastropods are ideal subjects on which to explore these patterns, by virtue of the remarkable intraspecific variation in life‐history traits and morphology often observed across relatively small spatial scales. The ubiquitous N‐Atlantic common whelk (Buccinum undatum) is well known for spatial variation in life‐history traits and morphology. Previous studies on genetic population structure have revealed that it exhibits significant differentiation across geographic distances. Within Breiðafjörður Bay, a large and shallow bay in W‐Iceland, genetic differentiation was demonstrated between whelks from sites separated by just 20 km. Here, we extended our previous studies on the common whelk in Breiðafjörður Bay by quantifying phenotypic variation in shell morphology and color throughout the Bay. We sought to test whether trait differentiation is dependent on geographic distance and/or environmental variability. Whelk in Breiðafjörður Bay displayed fine‐scale patterns of spatial variation in shape, thickness, and color diversity. Differentiation increased with increasing distance between populations, indicating that population connectivity is limited. Both shape and color varied along a gradient from the inner part of the bay in the east to the outer part in the west. Whelk shells in the innermost part of Breiðafjörður Bay were thick with an elongate shell, round aperture, and low color diversity, whereas in the outer part of the bay the shells were thinner, rounder, with a more elongate aperture and richer color diversity. Significant site‐specific difference in shell traits of the common whelk in correlation with environmental variables indicates the presence of local ecotypes and limited demographic connectivity.     

Qualitative and quantitative methods show stability in patterns of Cepaea nemoralis shell polymorphism in the Pyrenees over five decades

Over the past century, the study of animal color has been critical in establishing some of the founding principles of biology, especially in genetics and evolution. In this regard, one of the emerging strengths of working with the land snail genus Cepaea is that historical collections can be compared against modern‐day samples, for instance, to understand the impact of changing climate and habitat upon shell morph frequencies. However, one potential limitation is that prior studies scored shell ground color by eye into three discrete colours yellow, pink, or brown. This incurs both potential error and bias in comparative surveys. In this study, we therefore aimed to use a quantitative method to score shell color and evaluated it by comparing patterns of C. nemoralis shell color polymorphism in the Pyrenees, using both methods on present‐day samples, and against historical data gathered in the 1960s using the traditional method. The main finding was that while quantitative measures of shell color reduced the possibility of error and standardized the procedure, the same altitudinal trends were recovered, irrespective of the method. The results also showed that there was a general stability in the local shell patterns over five decades, including altitudinal clines, with just some exceptions. Therefore, although subject to potential error human scoring of snail color data remains valuable, especially if persons have appropriate training. In comparison, while there are benefits in taking quantitative measures of color in the laboratory, there are also several practical disadvantages, mainly in terms of throughput and accessibility. In the future, we anticipate that genomic methods may be used to understand the potential role of selection in maintaining shell morph clines. In addition, photographs generated by citizen scientists conducting field surveys may be used with deep learning‐based methods to survey color patterns.

We used a quantitative method to score the shell colour of Cepaea nemoralis shells, and evaluated it by comparing patterns shell colour polymorphism in the Pyrenees, using both methods on present day samples, and against historical data gathered in the 1960s using the traditional method. The main finding was that while quantitative measures of shell colour reduced the possibility of error and standardised the procedure, the same altitudinal trends were recovered, irrespective of the method. The results also showed that there was a general stability in the local shell patterns over five decades, including altitudinal clines, with just some exceptions.     

Quantitative genetics of human skin color

Skin color has long been of interest to human geneticists and often used as an example of a human quantitative trait under relatively wellunderstood genetic control. Although the basic biology of melanin production and the method of measurement are areas in which skin color studies are fairly well advanced, compared to other quantitative traits, the evolutionary significance and mode of inheritance are still being debated. In view of the many steps involved in the production and dispersion of melanin and the large number of loci involved in coat color of laboratory animals, it is suggested that genetic control of human skin color must be fairly complex. Studies that have found evidence for relatively few loci effecting the differences between racial groups may either be using inappropriate methods, or they may be concentrating attention on only that portion of genetic variability that distinguishes between major world groups, particularly blacks and whites. Genetic analysis of intermediate groups and pedigree analysis of rare pigmentation conditions may yield more information on skin color genetics.     

Gonadogenesis and color characteristics of ovaries in Japanese mitten crab <Emphasis Type="Italic">Eriocheir japonicus</Emphasis>

The gonadogenesis was studied in adult and juvenile females of Japanese mitten crab Eriocheir japonicus (Crustacea: Decapoda, Grapsida) inhabiting the rivers of the Maritime Territory. The morphometric parameters of oocytes at different stages of maturity were determined using the methods of computer morphometry and color characteristics were evaluated using the Munsell Book of Color. As a result, a color table was compiled for the ovaries from the beginning of development to gonad maturity, which included light yellow (sandy), yellow, beige, light purple, light brown, dark purple, brown (chocolate), and dark brown (brown). The regular changes in the ovary color of E. japonicus proved to closely correlate with the gonadogenesis, namely, with the composition of cells at each stage of gonad maturity.     

Flower color affects tri-trophic-level biocontrol interactions

The adults of many parasitoid species require nectar for optimal fitness, but very little is known of flower recognition. Flight cage experiments showed that the adults of an egg parasitoid (Trichogramma carverae Oatman and Pinto) benefited from alyssum (Lobularia maritima L.) bearing white flowers to a greater extent than was the case for light pink, dark pink or purple flowered cultivars, despite all cultivars producing nectar. Survival and realised parasitism on all non-white flowers were no greater than when the parasitoids were caged on alyssum shoots from which flowers had been removed. The possibility that differences between alyssum cultivars were due to factors other than flower color, such as nectar quality, was excluded by dying white alyssum flowers by placing the roots of the plants in 5% food dye (blue or pink) solution. Survival of T. carverae was lower on dyed alyssum flowers than on undyed white flowers. Mixing the same dyes with honey in a third experiment conducted in the dark showed that the low level of feeding on dyed flowers was unlikely to be the result of olfactory or gustatory cues. Flower color appears, therefore, to be a critical factor in the choice of plants used to enhance biocontrol, and is likely also to be a factor in the role parasitoids play in structuring invertebrate communities.     

Additional betalain accumulation by genetic engineering leads to a novel flower color in lisianthus (Eustoma grandiflorum)

Betalains, comprising violet betacyanins and yellow betaxanthins, are pigments found in plants belonging to the order Caryophyllales. In this study, we induced the accumulation of betalains in ornamental lisianthus (Eustoma grandiflorum) by genetic engineering. Three betalain biosynthetic genes encoding CYP76AD1, dihydroxyphenylalanine (DOPA) 4,5-dioxygenase (DOD), and cyclo-DOPA 5-O-glucosyltransferase (5GT) were expressed under the control of the cauliflower mosaic virus (CaMV) 35S promoter in lisianthus, in which anthocyanin pigments are responsible for the pink flower color. During the selection process on hygromycin-containing media, some shoots with red leaves were obtained. However, most red-colored shoots were suppressed root induction and incapable of further growth. Only clone #1 successfully acclimatized and bloomed, producing pinkish-red flowers, with a slightly greater intensity of red color than that in wild-type flowers. T₁ plants derived from clone #1 segregated into five typical flower color phenotypes: wine red, bright pink, pale pink, pale yellow, and salmon pink. Among these, line #1-1 showed high expression levels of all three transgenes and exhibited a novel wine-red flower color. In the flower petals of line #1-1, abundant betacyanins and low-level betaxanthins were coexistent with anthocyanins. In other lines, differences in the relative accumulation of betalain and anthocyanin pigments resulted in flower color variations, as described above. Thus, this study is the first to successfully produce novel flower color varieties in ornamental plants by controlling betalain accumulation through genetic engineering.